This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.
- Johannes Köster (@johanneskoester)
If you simply want to use this workflow, download and extract the latest release. If you intend to modify and further develop this workflow, fork this repository. Please consider providing any generally applicable modifications via a pull request.
In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, if available, its DOI (see above).
Configure the workflow according to your needs via editing the file config.yaml.
Test your configuration by performing a dry-run via
snakemake -n
Execute the workflow locally via
snakemake --cores $N
using $N cores or run it in a cluster environment via
snakemake --cluster qsub --jobs 100
or
snakemake --drmaa --jobs 100
See the Snakemake documentation for further details and other options (e.g. Cloud execution).
After successful execution, you can create a self-contained report with all results via:
snakemake --report report.html
Example output from our test dataset can be seen here.
Tests cases are in the subfolder .test. They should be executed via continuous integration with Travis CI.